Mercurial > repos > iuc > transdecoder
annotate transdecoder.xml @ 6:d0d4cef4f967 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
author | iuc |
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date | Mon, 01 Feb 2021 20:51:40 +0000 |
parents | c6334cb383ff |
children | ffd1300599a1 |
rev | line source |
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c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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1 <tool id="transdecoder" name="TransDecoder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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2 <description>finds coding regions within transcripts</description> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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3 <macros> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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4 <token name="@TOOL_VERSION@">5.5.0</token> |
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d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
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5 <token name="@VERSION_SUFFIX@">1</token> |
5
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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6 </macros> |
0
8aef9a17faae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
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7 <requirements> |
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c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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8 <requirement type="package" version="@TOOL_VERSION@">transdecoder</requirement> |
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d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents:
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9 <requirement type="package" version="3.0">zip</requirement> |
0
8aef9a17faae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
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10 </requirements> |
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c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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11 <version_command><![CDATA[TransDecoder.LongOrfs --version 2>&1 | grep 'TransDecoder.LongOrfs' | cut -f 2 -d ' ']]></version_command> |
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0db979fead3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit f0e5f4748034bc0f1faafcec65bffa34b64a4781
iuc
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12 <command detect_errors="exit_code"><![CDATA[ |
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c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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13 ## initialize |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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14 ln -s '${t}' 'transcripts.fasta' && |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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15 |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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16 ## run TransDecoder.LongOrfs |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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17 TransDecoder.LongOrfs |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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18 ## Shared options |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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19 -t 'transcripts.fasta' |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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20 -G '${G}' |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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21 ## LongOrfs options |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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22 #if $lo.gene_trans_map |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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23 --gene_trans_map '${lo.gene_trans_map}' |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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24 #end if |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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25 -m $lo.m |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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26 ${lo.S} |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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27 -O 'output' ## required, otherwise value of -t is used as output folder |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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28 |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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29 ## run TransDecoder.Predict |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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30 #if $po.predict_cond.predict_sel == 'yes' |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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31 && TransDecoder.Predict |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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32 ## Shared options |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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33 -t 'transcripts.fasta' |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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34 -G '${G}' |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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35 ## Predict options |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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36 --retain_long_orfs_mode $po.predict_cond.mode_cond.mode_sel |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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37 #if $po.predict_cond.mode_cond.mode_sel == 'strict' |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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38 --retain_long_orfs_length $po.predict_cond.mode_cond.retain_long_orfs_length |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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39 #end if |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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40 #if $po.predict_cond.retain_pfam_hits |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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41 --retain_pfam_hits '$po.predict_cond.retain_pfam_hits' |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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42 #end if |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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43 #if $po.predict_cond.retain_blastp_hits |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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44 --retain_blastp_hits '$po.predict_cond.retain_blastp_hits' |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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45 #end if |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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46 $po.predict_cond.single_best_only |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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47 $po.predict_cond.no_refine_starts |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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48 -T $po.predict_cond.T |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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49 -O 'output' |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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50 #end if |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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51 |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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52 ## postprocessing |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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53 #if 'log' in $oo.out |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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54 |& tee '$out_log' |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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55 #end if |
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d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
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56 && if ls 'output/'*'.pdf' >/dev/null 2>&1; then zip 'seqlogo.zip' 'output/'*'.pdf' -q -j; fi |
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8aef9a17faae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
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57 ]]></command> |
8aef9a17faae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
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58 <inputs> |
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c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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59 <param argument="-t" type="data" format="fasta" label="Select file with transcripts"/> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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60 <param argument="-G" type="select" label="Select genetic code"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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61 <option value="Acetabularia">Acetabularia</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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62 <option value="Candida">Candida</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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63 <option value="Ciliate">Ciliate</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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64 <option value="Dasycladacean">Dasycladacean</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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65 <option value="Euplotid">Euplotid</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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66 <option value="Hexamita">Hexamita</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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67 <option value="Mesodinium">Mesodinium</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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68 <option value="Mitochondrial-Ascidian">Mitochondrial-Ascidian</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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69 <option value="Mitochondrial-Chlorophycean">Mitochondrial-Chlorophycean</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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70 <option value="Mitochondrial-Echinoderm">Mitochondrial-Echinoderm</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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71 <option value="Mitochondrial-Flatworm">Mitochondrial-Flatworm</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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72 <option value="Mitochondrial-Invertebrates">Mitochondrial-Invertebrates</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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73 <option value="Mitochondrial-Protozoan">Mitochondrial-Protozoan</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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74 <option value="Mitochondrial-Pterobranchia">Mitochondrial-Pterobranchia</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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75 <option value="Mitochondrial-Scenedesmus_obliquus">Mitochondrial-Scenedesmus_obliquus</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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76 <option value="Mitochondrial-Thraustochytrium">Mitochondrial-Thraustochytrium</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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77 <option value="Mitochondrial-Trematode">Mitochondrial-Trematode</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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78 <option value="Mitochondrial-Vertebrates">Mitochondrial-Vertebrates</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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79 <option value="Mitochondrial-Yeast">Mitochondrial-Yeast</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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80 <option value="Pachysolen_tannophilus">Pachysolen_tannophilus</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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81 <option value="Peritrich">Peritrich</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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82 <option value="SR1_Gracilibacteria">SR1_Gracilibacteria</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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83 <option value="Tetrahymena">Tetrahymena</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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84 <option value="Universal" selected="true">Universal</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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85 </param> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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86 <section name="lo" title="LongOrfs options" expanded="true"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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87 <param argument="--gene_trans_map" type="data" format="tabular" optional="true" label="Select gene-to-transcript identifier mapping file" help="gene_id<tab>trans_id<return>"/> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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88 <param argument="-m" type="integer" value="100" min="1" label="Set minimum protein length"/> |
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d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
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89 <param argument="-S" type="boolean" truevalue="-S" falsevalue="" label="Activate strand-specificity?" help="Only analyse top strand?"/> |
5
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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90 </section> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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91 <section name="po" title="Predict options" expanded="true"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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92 <!-- |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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93 TransDecoder.Predict can be skipped if only longest_orfs.pep (as a result of TransDecoder.LongOrfs) is required, e.g. for homology search via BlastP and Pfam. |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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94 --> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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95 <conditional name="predict_cond"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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96 <param name="predict_sel" type="select" label="Should likely coding regions be predicted?" help="(TransDecoder.Predict)"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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97 <option value="yes" selected="true">Yes</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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98 <option value="no">No</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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99 </param> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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100 <when value="yes"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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101 <conditional name="mode_cond"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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102 <param argument="mode_sel" type="select" label="Select mode to retain long ORFs" help="In dynamic mode: set range according to 1% FDR in a random sequence of same GC content."> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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103 <option value="dynamic" selected="true">Dynamic</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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104 <option value="strict">Strict</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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105 </param> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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106 <when value="dynamic"/> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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107 <when value="strict"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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108 <param argument="--retain_long_orfs_length" type="integer" value="1000000" min="0" label="Set long ORFs length" help="Retain all ORFs found that are equal or longer than these many nucleotides even if no other evidence marks it as coding."/> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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109 </when> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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110 </conditional> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
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111 <param argument="--retain_blastp_hits" type="data" format="tabular" optional="true" label="Select BlastP result file" help="Any ORF with a blast match will be retained in the final output. (tabular outfmt6 file)"/> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
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112 <param argument="--retain_pfam_hits" type="data" format="tabular" optional="true" label="Select Pfam result file" help="Domain table output file from running hmmscan to search Pfam. Any ORF with a pfam domain hit will be retained in the final output. (tabular domtblout file)"/> |
5
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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113 <param argument="--single_best_only" type="boolean" truevalue="--single_best_only" falsevalue="" label="Retain only the single best ORF per transcript?" help="Prioritized by homology than ORF length."/> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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114 <param argument="--no_refine_starts" type="boolean" truevalue="--no_refine_starts" falsevalue="" label="Start refinement that identifies potential start codons for 5' partial ORFs using a PWM?"/> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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115 <param argument="-T" type="integer" value="500" min="1" label="Set top longest ORFs to train Markov Model" help="The first (10*value) elements are selected for removing redundancies. Then number of longst ORFs of this value are selected from the non-redundant set."/> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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116 </when> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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117 <when value="no"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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118 </conditional> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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119 </section> |
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d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
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120 <section name="oo" title="Output options" expanded="true"> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
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121 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)" help="Only shown in history if selected here and generated by the specific run."> |
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c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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122 <!-- LongOrfs --> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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123 <option value="lo_cds">Longest ORFs (CDS)</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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124 <option value="lo_gff3">Longest ORFs (GFF3)</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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125 <option value="lo_pep" selected="true">Longest ORFs (PEP)</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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126 <!-- Predict --> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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127 <option value="bed" selected="true">Results (BED)</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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128 <option value="cds" selected="true">Results (CDS)</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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129 <option value="gff3" selected="true">Results (GFF3)</option> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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130 <option value="pep" selected="true">Results (PEP)</option> |
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d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
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131 <option value="plot">Plots</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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132 <!-- Others --> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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133 <option value="log">Log</option> |
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8aef9a17faae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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134 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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135 </section> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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136 </inputs> |
8aef9a17faae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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137 <outputs> |
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138 <!-- LongOrfs --> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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139 <data name="out_lo_cds" format="fasta" from_work_dir="output/longest_orfs.cds" label="${tool.name} on ${on_string}: Longest ORFs (CDS/FASTA)"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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140 <filter>'lo_cds' in oo['out']</filter> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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141 </data> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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142 <data name="out_lo_gff3" format="gff3" from_work_dir="output/longest_orfs.gff3" label="${tool.name} on ${on_string}: Longest ORFs (GFF3)"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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143 <filter>'lo_gff3' in oo['out']</filter> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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144 </data> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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145 <data name="out_lo_pep" format="fasta" from_work_dir="output/longest_orfs.pep" label="${tool.name} on ${on_string}: Longest ORFs (PEP/FASTA)"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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146 <filter>'lo_pep' in oo['out']</filter> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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147 </data> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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148 <!-- Predict --> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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149 <data name="out_bed" format="bed" from_work_dir="transcripts.fasta.transdecoder.bed" label="${tool.name} on ${on_string}: Results (BED)"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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150 <filter>'bed' in oo['out'] and po['predict_cond']['predict_sel'] == 'yes'</filter> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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151 </data> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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152 <data name="out_cds" format="fasta" from_work_dir="transcripts.fasta.transdecoder.cds" label="${tool.name} on ${on_string}: Results (CDS/FASTA)"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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153 <filter>'cds' in oo['out'] and po['predict_cond']['predict_sel'] == 'yes'</filter> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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154 </data> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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155 <data name="out_gff3" format="gff3" from_work_dir="transcripts.fasta.transdecoder.gff3" label="${tool.name} on ${on_string}: Results (GFF3)"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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156 <filter>'gff3' in oo['out'] and po['predict_cond']['predict_sel'] =='yes'</filter> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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157 </data> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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158 <data name="out_pep" format="fasta" from_work_dir="transcripts.fasta.transdecoder.pep" label="${tool.name} on ${on_string}: Results (PEP/FASTA)"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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159 <filter>'pep' in oo['out'] and po['predict_cond']['predict_sel'] == 'yes'</filter> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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160 </data> |
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d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
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161 <data name="out_plot" format="zip" from_work_dir="seqlogo.zip" label="${tool.name} on ${on_string}: Plots"> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
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162 <filter>'plot' in oo['out'] and po['predict_cond']['predict_sel'] == 'yes'</filter> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
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163 </data> |
5
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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164 <!-- Others --> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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165 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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166 <filter>'log' in oo['out']</filter> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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167 </data> |
0
8aef9a17faae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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168 </outputs> |
8aef9a17faae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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169 <tests> |
5
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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170 <!-- #1 default --> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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171 <test expect_num_outputs="5"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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172 <param name="t" value="transcripts.fasta"/> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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173 <!-- LongOrfs --> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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174 <output name="out_lo_pep"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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175 <assert_contents> |
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d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
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176 <has_n_lines n="190"/> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
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177 <has_line line=">CUFF.20.1.p2 type:3prime_partial len:205 gc:Universal CUFF.20.1:612-1(-)"/> |
5
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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178 </assert_contents> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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179 </output> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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180 <!-- Predict --> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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181 <output name="out_bed"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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182 <assert_contents> |
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d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
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183 <has_n_lines n="81"/> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
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184 <has_text_matching expression="CUFF\.9\.1.+"/> |
5
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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185 </assert_contents> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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186 </output> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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187 <output name="out_cds"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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188 <assert_contents> |
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d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
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189 <has_n_lines n="1578"/> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
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190 <has_line line=">CUFF.9.1.p1 GENE.CUFF.9.1~~CUFF.9.1.p1 ORF type:complete len:156 (+),score=36.30 CUFF.9.1:173-640(+)"/> |
5
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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191 </assert_contents> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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192 </output> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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193 <output name="out_gff3"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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194 <assert_contents> |
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d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
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195 <has_n_lines n="542"/> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
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196 <has_text_matching expression="CUFF\.9\.1.+"/> |
5
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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197 </assert_contents> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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198 </output> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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199 <output name="out_pep"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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200 <assert_contents> |
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d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
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201 <has_n_lines n="608"/> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
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202 <has_text_matching expression="CUFF\.9\.1.+"/> |
5
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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203 </assert_contents> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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204 </output> |
0
8aef9a17faae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
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205 </test> |
5
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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206 <!-- #2 --> |
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d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
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207 <test expect_num_outputs="9"> |
5
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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208 <param name="t" value="transcripts.fasta"/> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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209 <param name="G" value="Acetabularia"/> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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210 <section name="lo"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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211 <param name="m" value="101"/> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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212 <param name="S" value="true"/> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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213 </section> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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214 <section name="po"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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215 <conditional name="predict_cond"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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216 <param name="predict_sel" value="yes"/> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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217 <conditional name="mode_cond"> |
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d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
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218 <param name="mode_sel" value="strict"/> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
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219 <param name="retain_long_orfs_length" value="1000001"/> |
5
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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220 </conditional> |
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d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
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221 <param name="retain_blastp_hits" value="blastp.outfmt6"/> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
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222 <param name="retain_pfam_hits" value="pfam.domtblout"/> |
5
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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223 <param name="single_best_only" value="true"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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224 <param name="no_refine_starts" value="true"/> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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225 <param name="T" value="501"/> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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226 </conditional> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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227 </section> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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228 <section name="oo"> |
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d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
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229 <param name="out" value="lo_pep,lo_gff3,lo_cds,bed,cds,gff3,pep,plot,log"/> |
5
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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230 </section> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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231 <!-- LongOrfs --> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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232 <output name="out_lo_cds"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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233 <assert_contents> |
6
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents:
5
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234 <has_n_lines n="398"/> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents:
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235 <has_text_matching expression="CUFF\.20\.1.+"/> |
5
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
4
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236 </assert_contents> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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237 </output> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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238 <output name="out_lo_gff3"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
4
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239 <assert_contents> |
6
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents:
5
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240 <has_n_lines n="1330"/> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents:
5
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241 <has_text_matching expression="CUFF\.20\.1.+"/> |
5
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
4
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242 </assert_contents> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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243 </output> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
4
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244 <output name="out_lo_pep"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
4
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245 <assert_contents> |
6
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents:
5
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246 <has_n_lines n="398"/> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents:
5
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247 <has_text_matching expression="CUFF\.20\.1.+"/> |
5
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
4
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248 </assert_contents> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
4
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249 </output> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
4
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250 <!-- Predict --> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
4
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251 <output name="out_bed"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
4
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252 <assert_contents> |
6
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents:
5
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253 <has_n_lines n="62"/> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents:
5
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|
254 <has_text_matching expression="CUFF\.9\.1.+"/> |
5
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
4
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255 </assert_contents> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
4
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256 </output> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
4
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257 <output name="out_cds"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
4
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258 <assert_contents> |
6
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents:
5
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|
259 <has_n_lines n="1312"/> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents:
5
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260 <has_text_matching expression="CUFF\.9\.1.+"/> |
5
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
4
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261 </assert_contents> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
4
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262 </output> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
4
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|
263 <output name="out_gff3"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
4
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264 <assert_contents> |
6
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents:
5
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|
265 <has_n_lines n="395"/> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents:
5
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266 <has_text_matching expression="CUFF\.9\.1.+"/> |
5
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
4
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267 </assert_contents> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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268 </output> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
4
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269 <output name="out_pep"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
4
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270 <assert_contents> |
6
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents:
5
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271 <has_n_lines n="500"/> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents:
5
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272 <has_text_matching expression="CUFF\.9\.1.+"/> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents:
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273 </assert_contents> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents:
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274 </output> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents:
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275 <output name="out_plot"> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents:
5
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276 <assert_contents> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents:
5
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277 <has_size value="0"/> |
5
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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278 </assert_contents> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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279 </output> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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280 <!-- Others --> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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281 <output name="out_log"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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282 <assert_contents> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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283 <has_text_matching expression="transdecoder is finished.+"/> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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284 </assert_contents> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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285 </output> |
0
8aef9a17faae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
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286 </test> |
5
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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287 <!-- #3 --> |
6
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents:
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288 <test expect_num_outputs="9"> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents:
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289 <param name="t" value="pasa_assemblies.fasta"/> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents:
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290 <section name="lo"> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents:
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291 <param name="gene_trans_map" value="pasa_genetransmap.txt"/> |
5
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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292 </section> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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293 <section name="oo"> |
6
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents:
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294 <param name="out" value="lo_pep,lo_gff3,lo_cds,bed,cds,gff3,pep,plot,log"/> |
5
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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295 </section> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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296 <!-- LongOrfs --> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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changeset
|
297 <output name="out_lo_cds"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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298 <assert_contents> |
6
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents:
5
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299 <has_n_lines n="534"/> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents:
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300 <has_text_matching expression=">asmbl\_236\.p1.+"/> |
5
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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301 </assert_contents> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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302 </output> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
4
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|
303 <output name="out_lo_gff3"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
4
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304 <assert_contents> |
6
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents:
5
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changeset
|
305 <has_n_lines n="1742"/> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents:
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|
306 <has_text_matching expression="asmbl\_236.+"/> |
5
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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|
307 </assert_contents> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
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308 </output> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
4
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changeset
|
309 <output name="out_lo_pep"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
parents:
4
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|
310 <assert_contents> |
6
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
parents:
5
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311 <has_n_lines n="534"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
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312 <has_text_matching expression=">asmbl\_236\.p1.+"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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313 </assert_contents> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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314 </output> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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315 <!-- Predict --> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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316 <output name="out_bed"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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317 <assert_contents> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
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318 <has_n_lines n="204"/> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
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319 <has_text_matching expression="asmbl\_99.+"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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320 </assert_contents> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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321 </output> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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322 <output name="out_cds"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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323 <assert_contents> |
6
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
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324 <has_n_lines n="3560"/> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
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325 <has_text_matching expression=">asmbl\_99\.p1.+"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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326 </assert_contents> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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327 </output> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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328 <output name="out_gff3"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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329 <assert_contents> |
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d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
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330 <has_n_lines n="1337"/> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
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331 <has_text_matching expression="asmbl\_99.+"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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332 </assert_contents> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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333 </output> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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334 <output name="out_pep"> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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335 <assert_contents> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
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336 <has_n_lines n="1391"/> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
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337 <has_text_matching expression=">asmbl\_99\.p1.+"/> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
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338 </assert_contents> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
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339 </output> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
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340 <output name="out_plot"> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
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341 <assert_contents> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
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342 <has_size value="714868" delta="1000"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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343 </assert_contents> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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344 </output> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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345 <!-- Others --> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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346 <output name="out_log"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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347 <assert_contents> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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348 <has_text_matching expression="transdecoder is finished.+"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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349 </assert_contents> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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350 </output> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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351 </test> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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352 <!-- #4 --> |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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353 <test expect_num_outputs="1"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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354 <param name="t" value="transcripts.fasta"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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355 <section name="po"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
iuc
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356 <conditional name="predict_cond"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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357 <param name="predict_sel" value="no"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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358 </conditional> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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359 </section> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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360 <!-- LongOrfs --> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
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361 <output name="out_pep"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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362 <assert_contents> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
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363 <has_n_lines n="190"/> |
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
iuc
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364 <has_text_matching expression="CUFF\.9\.1.+"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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365 </assert_contents> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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366 </output> |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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367 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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368 </tests> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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369 <help><![CDATA[ |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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370 .. class:: infomark |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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371 |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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372 **What it does** |
8aef9a17faae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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373 |
5
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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374 TransDecoder identifies candidate coding regions within transcript sequences such as those generated by de novo RNA-Seq transcript assembly using Trinity or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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375 |
8aef9a17faae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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376 TransDecoder identifies likely coding sequences based on the following criteria: |
8aef9a17faae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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377 |
5
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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378 - a minimum length open reading frame (ORF) is found in a transcript sequence. |
0
8aef9a17faae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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379 - a log-likelihood score similar to what is computed by the GeneID software is > 0. |
8aef9a17faae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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380 - the above coding score is greatest when the ORF is scored in the 1st reading frame as compared to scores in the other 5 reading frames. |
8aef9a17faae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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381 - if a candidate ORF is found fully encapsulated by the coordinates of another candidate ORF, the longer one is reported. However, a single transcript can report multiple ORFs (allowing for operons, chimeras, etc). |
5
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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382 - a PSSM is built/trained/used to refine the start codon prediction. |
0
8aef9a17faae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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383 - optional the putative peptide has a match to a Pfam domain above the noise cutoff score. |
8aef9a17faae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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384 |
5
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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385 *Step 1*: Extract long open reading frames |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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386 |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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387 By default, TransDecoder.LongOrfs will identify ORFs that are at least 100 amino acids long. You can lower this via the '-m' parameter, but know that the rate of false positive ORF predictions increases drastically with shorter minimum length criteria. |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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388 |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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389 *Step 2*: (optional and not part of this wrapper) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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390 |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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391 The result "longest ORFs (PEP)" can be used to identify ORFs with homology to known proteins via BlastP or Pfam searches (`details <https://github.com/TransDecoder/TransDecoder/wiki#including-homology-searches-as-orf-retention-criteria>`_). |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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392 |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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393 *Step 3*: Predict the likely coding regions |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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394 |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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395 Optionally apply results of homology searches in this step and re-run the whole analysis. |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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396 |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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397 **Input** |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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398 |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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399 - FASTA file with transcripts |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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400 - (optional) gene-to-transcript identifier mapping file |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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401 - (optional) BLAST or Pfam database file (`details <https://github.com/TransDecoder/TransDecoder/wiki#including-homology-searches-as-orf-retention-criteria>`_) |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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402 |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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403 **Output** |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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404 |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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405 *LongOrfs* |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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406 |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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407 - longest ORFs (PEP/FASTA): all ORFs meeting the minimum length criteria, regardless of coding potential |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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408 - longest ORFs (GFF3): positions of all ORFs as found in the target transcripts |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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409 - longest ORFs (CDS/FASTA): the nucleotide coding sequence for all detected ORFs |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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410 |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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411 *Predict* |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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412 |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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413 - Results (PEP/FASTA): peptide sequences for the final candidate ORFs; all shorter candidates within longer ORFs were removed |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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414 - Results (CDS/FASTA): nucleotide sequences for coding regions of the final candidate ORFs |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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415 - Results (GFF3): positions within the target transcripts of the final selected ORFs |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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416 - Results (BED): BED-formatted file describing ORF positions, best for viewing using GenomeView or IGV |
6
d0d4cef4f967
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
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417 - Plots: sequence logos and scores (compressed PDF) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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418 |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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419 *Other* |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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420 |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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421 - Log file |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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422 |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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423 .. class:: infomark |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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424 |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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425 **References** |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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426 |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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427 More information are available on `GitHub <https://github.com/TransDecoder/TransDecoder>`_. |
c6334cb383ff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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428 ]]></help> |
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0db979fead3a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit f0e5f4748034bc0f1faafcec65bffa34b64a4781
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429 <citations> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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430 <citation type="doi">10.1038/nprot.2013.084</citation> |
8aef9a17faae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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431 </citations> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d"
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432 </tool> |